[ensembl-dev] Ensembl REST API > possible bug in LD endpoints

[Ramiro Magno]

Hi devs,

When looking for proxy snps of rs7707921, the snp rs17243791 does not show
up:

https://rest.ensembl.org/ld/homo_sapiens/rs7707921/1000GENOMES:phase_3:CEU?window_size=500;d_prime=0;r2=0.8

But if I ask for their linkage disequilibrium explicitly:

https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs17243791?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0

I can see that they are indeed in LD with an r^2 of 0.920 (above the 0.8
threshold used above).

The two snps are 215,400 bp away from each other, which is below the 250k
up/downstream threshold, i.e. window_size=500.

Any clue?

Many thanks in advance, Ramiro Magno
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